[gmx-users] Still force field issues: dihedral angle parameters

[Marc Baaden]

>>> "Berk Hess" said:
 >> The huge topology table in the paper manual gives all units
 >> of all forcefield parameters. In the 3.1 manual this is on
 >> pages 94 and 95. The table also specifies on which two atoms
 >> the dihedral parameters depend. For proper and RB dihedrals
 >> these are the inner two. This is because the effect of the
 >> outer two atoms should be incorporated in the pair (1-4)
 >> interactions.

OK, sorry I did miss the (immense value of the) table.


 >> The dihedral type does not imply 1-4 exclusions. The exclusions
 >> are defined on the moleculetype line in the molecule definition.

OK, but my point is that I don't understand why the manual on page 59 says
"with the Ryckaert-Bellemans potential the 1-4 interactions must be excluded
from the non-bonded list." (btw, this remark is repeated 3 times, so I guess
there was supposed to be some emphasis on it ?)
To my knowledge in other forcefields (Amber, MM3, ..) RB type dihedral
potentials (in the form of a series expansion of the 1-cos(n p - p0) term)
and 1,4-LJ interactions are used simultaneously.

Also, this opens another question: if you know what your dihedral angle
potential is supposed to look like, how do you derive corresponding
dihedral and LJ-1,4 parameters (eg how do you separate the function
V(phi) for i-j-k-l into V_dihedral(j-k) and V_LJ,1-4(i-l) ?


A last question (I hope) on dihedrals:
If I use  [ dihedrals ] to define eg 2 or more entries for the same
dihedral angle, will I get a sum of several cosine terms for that bond ?
(which would be a sort of faking a multiple term cosines series)

Cheers,
Marc

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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